Publications

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Hannenhalli S, Russell RB.  2000.  Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular Biology. 303(1):61-76.
Hannenhalli S, Levy S.  2001.  Promoter prediction in the human genome. Bioinformatics. 17(Suppl 1):S90-S96-S90-S96.
Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000:184-202.
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77:1-19.
Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM. 46(1):1-27.
Hannenhalli S.  2007.  Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational genomics: current methods. :21-21.
Hannenhalli S.  2006.  Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06). :31-31.
Hannenhalli S, Levy S.  2002.  Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.. 30(19):4278-4284.
Hannenhalli S, Pevzner P.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms. :304-313.
Hannenhalli S, Pevzner PA.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on. :581-581.
Hannenhalli S, Wang L-S.  2005.  Enhanced position weight matrices using mixture models. Bioinformatics. 21(Suppl 1):i204-i212-i204-i212.
Hannenhalli S, Pevzner P.  1995.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Proceedings of the twenty-seventh annual ACM symposium on Theory of computing. :178-189.
Hannenhalli S, Chappey C, Koonin EV, Pevzner PA.  1995.  Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. Genomics. 30(2):299-311.
Hannenhalli S.  1996.  Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied Mathematics. 71(1–3):137-151.
Hannenhalli S, Hayes WS, Hatzigeorgiou AG, Fickett JW.  1999.  Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.. 27(17):3577-3582.
Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA.  1996.  Positional sequencing by hybridization. Computer applications in the biosciences : CABIOS. 12(1):19-24.
Hannenhalli S, Kaestner KH.  2009.  The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev Genet. 10(4):233-240.
Hannenhalli S, Middleton RP, Levy S, Perroud B, Holzwarth JA, McDonald K, Hannah SS.  2006.  Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and Cartilage. 14(8):830-838.
Hannenhalli S.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 937:162-176.
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformatics. 24(11):1325-1331.
Hannenhalli S, Russell RB.  2001.  Analysis and prediction of protein functional sub-types from protein sequence alignments. EP20000203764(EP1096411)
Hannenhalli S, Levy S.  2003.  Transcriptional regulation of protein complexes and biological pathways. Mammalian Genome. 14(9):611-619.
Hannenhalli S, Perumalla K, Chandrasekharan N, Sridhar R.  1993.  A distributed algorithm for ear decomposition. , Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93. :180-184.
Hannuksela J, Sangi P, Heikkila J, Liu X, Doermann D.  2007.  Document Image Mosaicing with Mobile Phones. International Conference on Image Analysis and Processing (ICIAP'07). :1-8.
Hansel D, Cleaveland R, Smolka SA.  2004.  Distributed prototyping from validated specifications. Journal of Systems and Software. 70(3):275-298.

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